Transcriptome sequencing of sea cucumber (Apostichopus japonicus) and the identification of gene‐associated markers

Abstract

Sea cucumber (Apostichopus japonicus) is an ecologically and economically important species in East and South-East Asia. This project aimed to identify large numbers of gene-associated markers and differentially expressed genes (DEGs) after lipopolysaccharides (LPS) challenge in A.japonicus using high-throughput transcriptome sequencing. A total of 162 million high-quality reads of 174 million raw reads were obtained by deep sequencing using Illumina HiSeq™ 2000 platform. Assembly of these reads generated 94704 unigenes, with read length ranging from 200 to 16153bp (average length of 810bp). A total of 36005 were identified as coding sequences (CDSs), 32479 of which were successfully annotated. Based on the assembly transcriptome, we identified 142511 high-quality single nucleotide polymorphisms (SNPs). Among them, 33775, 63120 and 45616 were located in sequences without predicted CDS (non-CDSs), CDSs and untranslated regions (UTRs), respectively. These putative SNPs included 82664 transitions and 59847 transversions. Totally, 89375 (59.1%) were distributed in 15473 known genes. A total of 6417 microsatellites were detected in 5970 unigenes, 3216 of which were annotated and 2481 were successfully subjected for primer design. The numbers of simple sequence repeats (SSRs) identified in non-CDSs, CDSs and UTRs were 2367, 2316 and 1734. These potential SNPs and SSRs are expected to provide abundant resources for genetic, evolutionary and ecological studies in sea cucumber. Transcriptome comparison revealed 1330, 1347 and 1291 DEGs in the coelomocytes of A.japonicus at 4h, 24h and 72h after LPS challenge, respectively. Approximately 58.4% (1802) of total DEGs have been successfully annotated.